Bailey Willis was born at his parents' country estate at Idlewild-on-Hudson, near Cornwall, New York in 1857. He was the son of Nathaniel Parker Willis, a poet and journalist, and Cornelia (Grinnell) Willis of the prominent New England Grinnell family. His maternal granduncle, Henry Grinnell, was a benefactor of Arctic expeditions. His mother was instrumental in nurturing young Willis's interest in nature and exploration. After his father's death when Willis was ten years old, his mother, concerned about her son's "tendency to dream ineffectually," decided to train him in the stern disciplines of mathematics and science (Willis, A Yanqui in Patagonia 4). At the age of thirteen, Willis began schooling in Germany, where he received rigorous Prussian education.
Returning to New York in 1874, Willis entered the School of Mines at Columbia University, graduating with degrees in Mining Engineering in 1878 and Civil Engineering in 1879. After graduation Willis worked as an assistant for Raphael Pumpelly, a prominent geologist, by estimating iron and coal resources for the Northern Pacific Railroad. Geological work in the Pacific Northwest convinced Willis to support the preservation of Mount Rainier and its surroundings. The Mount Rainier National Park was established by law in 1899.
In 1882 Willis married his cousin Altona Holstein Grinnell. After her death in 1896, he married Margaret Delight Baker, daughter of anatomist Frank Baker. Margaret assisted Willis as draftsman and secretary.
Willis first earned international recognition as a geologist in the field of structural geology. Following the bankruptcy of the Northern Pacific Railway in 1884, Willis worked on assignments from the United States Geological Survey. While working in the southern Appalachian Mountains, he became interested in what had caused folding and faulting. By using laboratory experiments, Willis investigated the conditions causing the deformation of strata and published his new interpretation of the deformation in the report "The Mechanics of Appalachian Structure" (1893). This study established him as one of the country's leading structural geologists. His later book Geologic Structures (1923) went into three editions.
In addition to geological studies in the United States, Willis actively engaged himself in foreign expeditions throughout his life. From 1903 to1904, Willis led a scientific expedition to China under the auspices of the Carnegie Institution of Washington. With Eliot Blackwelder, an associate geologist, and R. H. Sargent, a topographer, the expedition investigated the geomorphology, stratigraphy, and paleontology of the country. The result of the expedition appeared as Research in China in 1907, which won a gold medal from the Geographic Society of France. Furthermore, in recognition of this work, Willis was awarded an honorary doctorate by the University of Berlin in 1910. In the same year the Argentine government invited Willis to conduct a geological survey of Patagonia for the region's irrigation potential.
In 1915, at age 59, Willis accepted a position of Chairman of the Department of Geology at Stanford University, where he remained affiliated as a professor emeritus after his retirement. In California, Willis extended his research to the area of seismology, and served as President of the Seismological Society of America. Believing in the permanence of continents, he held an oppositional view to the continental drift theories. In 1949, Willis died in Palo Alto, California at age 91.